I own the original, the box one. I also work at EB, but this is still going to be a guess for the most part.

I'm pretty sure that the Box and non-Box are the exact same, the boxed one was pretty much just for the initial shipment, basically for those people who reserved the game. You also got a poster for pre-ordering the game.

The non-boxed one is just how they produced it after the initial shipment, and then when it went greatest hits (i'm pretty sure it's greatest hits now) they continued to make it without boxing it.

So in summary, there is no difference. It's the same game, the company just chose to produce it without the box to most likely save money.

Edit: The boxed one also might have been exclusive to EB Games, but I'm not sure because the game came out before GameStop bought out EB Games, and before the two were the same company it was rare for bigger titles (I.E. Square-Enix games) to be exclusive to only GameStop or EB. The normal case was probably what Wal-Mart and Best Buy had to sell though.

Boxed was for pre-Greatest Hits, period. There was no exclusivity bullshit, as I've seen that all over the place. After it went Greatest Hits, they took out the box, made that the actual cover (Rather than the plain one that was there before) and fit the manual in by stuffing it with the shrink wrap.